ID code: '1I6J' CHIRALITY (03 Nov 1998) Checks the chirality and the naming of substituents of chiral and prochiral centers in nucleic acid structures. The molecular structure is read from a PDB file. Only the first model is evaluated. ---------------------------------------------------------- Center Reference for correct naming ---------------------------------------------------------- C1' alpha/beta nomenclature of anomeric sugars, base in beta position in natural nucleosids. C2' IUPAC. 1983. Eur J Biochem, 131: 9-15. C3' IUPAC. 1983. Eur J Biochem, 131: 9-15. C4' IUPAC. 1983. Eur J Biochem, 131: 9-15. C5' IUPAC. 1983. Eur J Biochem, 131: 9-15. P Brookhaven PDB entry '1BNA', O1P -> major groove, O2P -> minor groove. ---------------------------------------------------------- Author: Peter Slickers (slickers@imb-jena.de) Biocomputing, IMB Jena, Germany --------------------------------------------------------------------------------- Seq No Atom Residue H1' base O4' H1' base C2' --------------------------------------------------------------------------------- 8 C1' G B 1 beta 4 9 7 30 C1' T B 2 beta 26 31 29 50 C1' C B 3 beta 46 51 49 69 C1' G B 4 beta 65 70 68 91 C1' T B 5 beta 87 92 90 111 C1' C B 6 beta 107 112 110 131 C1' G C 11 beta 127 132 130 153 C1' A C 12 beta 149 154 152 174 C1' C C 13 beta 170 175 173 193 C1' G C 14 beta 189 194 192 215 C1' A C 15 beta 211 216 214 236 C1' C C 16 beta 232 237 235 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G B 1 8 5 29 C2' T B 2 30 27 49 C2' C B 3 50 47 68 C2' G B 4 69 66 90 C2' T B 5 91 88 110 C2' C B 6 111 108 130 C2' G C 11 131 128 152 C2' A C 12 153 150 173 C2' C C 13 174 171 192 C2' G C 14 193 190 214 C2' A C 15 215 212 235 C2' C C 16 236 233 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G B 1 OK 3 6 7 27 C3' T B 2 OK 25 28 29 47 C3' C B 3 OK 45 48 49 66 C3' G B 4 OK 64 67 68 88 C3' T B 5 OK 86 89 90 108 C3' C B 6 OK 106 109 110 128 C3' G C 11 OK 126 129 130 150 C3' A C 12 OK 148 151 152 171 C3' C C 13 OK 169 172 173 190 C3' G C 14 OK 188 191 192 212 C3' A C 15 OK 210 213 214 233 C3' C C 16 OK 231 234 235 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G B 1 OK 5 2 4 25 C4' T B 2 OK 27 24 26 45 C4' C B 3 OK 47 44 46 64 C4' G B 4 OK 66 63 65 86 C4' T B 5 OK 88 85 87 106 C4' C B 6 OK 108 105 107 126 C4' G C 11 OK 128 125 127 148 C4' A C 12 OK 150 147 149 169 C4' C C 13 OK 171 168 170 188 C4' G C 14 OK 190 187 189 210 C4' A C 15 OK 212 209 211 231 C4' C C 16 OK 233 230 232 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G B 1 1 3 24 C5' T B 2 23 25 44 C5' C B 3 43 45 63 C5' G B 4 62 64 85 C5' T B 5 84 86 105 C5' C B 6 104 106 125 C5' G C 11 124 126 147 C5' A C 12 146 148 168 C5' C C 13 167 169 187 C5' G C 14 186 188 209 C5' A C 15 208 210 230 C5' C C 16 229 231 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 20 P T B 2 distorted distorted 6 21 22 23 40 P C B 3 distorted distorted 28 41 42 43 59 P G B 4 distorted distorted 48 60 61 62 81 P T B 5 distorted distorted 67 82 83 84 101 P C B 6 distorted distorted 89 102 103 104 121 P G C 11 distorted distorted 122 123 124 143 P A C 12 distorted distorted 129 144 145 146 164 P C C 13 distorted distorted 151 165 166 167 183 P G C 14 distorted distorted 172 184 185 186 205 P A C 15 distorted distorted 191 206 207 208 226 P C C 16 distorted distorted 213 227 228 229 ---------------------------------------------------------------------------------